Accuracy of genomic selection using different methods to define haplotypes.
Accuracy of genomic selection using different methods to define haplotypes.
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DOI：
10.1534/genetics.107.080838
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发表时间：
2008-01-01
期刊：
影响因子：
3.3
通讯作者：
Veerkamp, R F
中科院分区：
文献类型：
--
作者：
Calus, M P L;Meuwissen, T H E;Veerkamp, R F
基因组选择使用幼年动物的总育种值，根据整个基因组中大量估计的标记单倍型效应进行预测。对遗传力为50%和10%的性状，在不同的标记密度下，比较了包括大量标记在内的四种不同模型预测育种值的准确性。模型估计了(1)每个单标记等位基因[单核苷酸多态(SNP)1]，(2)由两个相邻标记等位基因构建的单倍型(SNP2)，以及(3)由2个或10个标记构建的单倍型，包括通过连锁不平衡和连锁分析(HAP_IBD2和HAP_IBD10)构建的单倍型之间的协方差。在3-M基因组上模拟了119到2343个多态SNPs。对于遗传力为10%的性状，模型之间的差异很小，并且没有一个模型在所有标记密度上产生最高的准确率。对于遗传力为50%的性状，在所有标记密度下，HAP_IBD10模型对幼年动物和表型动物的总育种值的估计精度最高。结果表明，基因组选择比传统选择具有更高的精确度，特别是对于低遗传力性状。
Genomic selection uses total breeding values for juvenile animals, predicted from a large number of estimated marker haplotype effects across the whole genome. In this study the accuracy of predicting breeding values is compared for four different models including a large number of markers, at different marker densities for traits with heritabilities of 50 and 10%. The models estimated the effect of (1) each single-marker allele [single-nucleotide polymorphism (SNP)1], (2) haplotypes constructed from two adjacent marker alleles (SNP2), and (3) haplotypes constructed from 2 or 10 markers, including the covariance between haplotypes by combining linkage disequilibrium and linkage analysis (HAP_IBD2 and HAP_IBD10). Between 119 and 2343 polymorphic SNPs were simulated on a 3-M genome. For the trait with a heritability of 10%, the differences between models were small and none of them yielded the highest accuracies across all marker densities. For the trait with a heritability of 50%, the HAP_IBD10 model yielded the highest accuracies of estimated total breeding values for juvenile and phenotyped animals at all marker densities. It was concluded that genomic selection is considerably more accurate than traditional selection, especially for a low-heritability trait.